Due to population growth and the subsequent increase in the demand for food, low carbon food chain production systems are a necessity to reduce the effects on climate change as much as possible. Urban agriculture is of great interest because of its potential in reducing the indirect CO2 emissions of a city's food supply by reducing transportation distances, the packaging required and the food losses that occur during transportation. However, intensive urban agriculture production, which often relies on the use of soilless substrates, requires synthetic fertilizers rich in nitrogen, resulting in N2O emissions. Presently, there is a lack of studies that determine the generation of N2O from soilless crops to properly account for their global warming potential. In this study, an open chamber system was used to quantify N2O emissions from lettuce crops with perlite bags as their substrate in a Mediterranean rooftop greenhouse located in the metropolitan area of Barcelona (Spain). N2O generation, through nitrifying and denitrifying reactions, was limited by assuring an aerobic environment, negligible water retention, the absence of NH3, and controlled dosage of NO3− in the most favorable pH conditions for plant assimilation. The emission factor (EF) measured for the soilless lettuce crop (0. 0072–0. 0085 kg N2O−1 per kg N−1) was half the EF of the IPCC method (0. 0125 kg N2O−1 per kg N−1) for soil crops, which is commonly used in life cycle assessment (LCA) studies to approximate direct N2O emissions, for lack of a better method. Using a more appropriate EF for an LCA study of a tomato crop grown under similar conditions to those used to generate the EF resulted in a 7. 5% reduction (0. 06 kg CO2 eq. per kilogram of tomato production) in total global warming potential. This study shows that soilless crops reduce N2O emissions when compared to conventional crops, making urban agriculture an attractive practice for reducing GHG emissions. The results highlight the need to determine a standard method for determining an EF applicable to soilless protected crops, which, based on the parameters described here, such as the type of substrate, fertilizers and irrigation system, would allow for a more accurate environmental evaluation of soilless conventional and urban crops.